Genetic and Evolutionary of M and ORF3 Genes of Porcine Epidemic Diarrhea Virus in Part Areas of Yunnan Province

Purpose To identify the mutation and genetic evolution of porcine epidemic diarrhea virus (PEDV) strains in part areas of Yunnan Province in 2022-2023.

Methods A total of 125 small intestinal tissues, feces and anal swabs from pigs suspected being infected with PEDV were collected from nine pig farms in multiple regions of Yunnan, the viral nucleic acid was extracted, the PEDV was screening by RT-PCR, and the M and ORF3 genes of PEDV-positive samples were amplified and sequenced. The PEDV reference in GenBank was used for genetic analysis, and the genetic and evolutionary tree was constructed by bioinformatics software, and the homology of nucleotide sequence and amino acid sequence was also analyzed.

Results A total of 49 PEDV-positive samples were obtained from five pig farms, with a positive rate of 39.2% (49/125); the positive rate of porcine rotavirus (PoRV) was 11.2% (14/125); the mixed infection rate of PoRV and PEDV was 10.4% (13/125); and no porcine infectious gastroenteritis virus (TGEV) and porcine delta coronavirus (PDCoV) were detected. Compared with the classic vaccine strain CV777, both the M gene and ORF3 gene of the 10 PEDV strains showed nucleotide and amino acid mutations. The homology analysis of M gene showed that all 10 strains belonged to GⅡ type, among which, YNQJF4-6 and YNQJF4-7 were closely related to AJ1102, GD-A and LC strains in China; and the remaining eight strains were closely related to GD S07. The nucleotide homology among M gene strains was 96.9%-100.0%, and there were multiple base mutations. The homology analysis of ORF3 gene showed that the nucleotide homology among strains was 95.6%-100.0%, and there were five amino acid mutation sites, with no amino acid insertion or deletion. Compared with the ORF3 protein amino acid sequences of DR13 and JS2008, the 10 strains did not have continuous large fragments of amino acid deletions, the prevalent PEDV strains were mostly highly virulent, and their M gene and ORF3 gene had mutations of different degrees, suggesting that PEDV was constantly evolving and mutating during prevalence.

Conclusion The emergence of virulent GⅡ-based strong strains in Yunnan pig herds, therefore, there is an urgent need to develop vaccines targeting variant strains to reduce the economic losses.